Polysaccharide Lyase Family 2

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• Author: ^^^Wade Abbott^^^
• Responsible Curator: ^^^Wade Abbott^^^

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Polysaccharide Lyase Family PL2
Mechanism	β-elimination
Metal Cofactor	Manganese
Active site residues	known
CAZy DB link
https://www.cazy.org/PL2.html

Substrate specificities

Activity have been demonstrated on homogalacturonan (pectate) and (α1,4)-linked oligogalacturonides [1, 2].

Kinetics and Mechanism

α1,4 of pectate involves a Bronstead base for proton abstraction (i.e. arginine), a catalytic metal for acidification of the β-proton and oxyanion stabilization. PL2s have reported pH optimas in the range of 7.4 - 9.6 [1, 3], substantially lower than the pKa of arginine. These effects have been attributed to localized pKa effects within the active site.

Catalytic Residues

Content is to be added here.

Subfamilies

Subfamily 1, associated with endo-activity is preferentially active on homogalacturonan. Subfamily

Three-dimensional structures

The structure of the endolytic PL2A from Yersinia enterocolitica (YePL2A) is the only only PL2 structure to be reported [1]. Three different models for YePL2A have been deposited, including a native-form (2V8I, 1.50 Å), and a complex with trigalacturonate (2V8K, 2.1 Å) and a transitional metal (2V8J, 2.01 Å). Family 2 PLs adopt a rare α/α-7 barrel fold, with an active site cleft extending along the surface of the enzyme between two catalytic arms. The active site centre, consisting of the metal coordination pocket and catalytic arginines, is positioned at one end of the cleft. Substrate binding induces a conformational change and the arms close about the substrate.

Family Firsts

First catalytic activity

PelY from Yersinia pseudotuberculosis macerated cucumber [4].

First catalytic base identification

YePL2A (YE4069) Arg218 from Yersinia enterocolitica [1].

First catalytic divalent cation identification

DdPL2/PelW(Dda3937_03361) from Dickeya Dadantii 3937 (Previously Erwinia chrysanthemi3937)[2].

First 3-D structure

PL2A (YE4069) from Yersinia enterocolitica [1].

References

1. Abbott DW and Boraston AB. (2007). A family 2 pectate lyase displays a rare fold and transition metal-assisted beta-elimination. J Biol Chem. 2007;282(48):35328-36. DOI:10.1074/jbc.M705511200 |
2. Shevchik VE, Condemine G, Robert-Baudouy J, and Hugouvieux-Cotte-Pattat N. (1999). The exopolygalacturonate lyase PelW and the oligogalacturonate lyase Ogl, two cytoplasmic enzymes of pectin catabolism in Erwinia chrysanthemi 3937. J Bacteriol. 1999;181(13):3912-9. DOI:10.1128/JB.181.13.3912-3919.1999 |
3. Abbott DW, Thomas D, Pluvinage B, and Boraston AB. (2013). An ancestral member of the polysaccharide lyase family 2 displays endolytic activity and magnesium dependence. Appl Biochem Biotechnol. 2013;171(7):1911-23. DOI:10.1007/s12010-013-0483-9 |
4. Manulis S, Kobayashi DY, and Keen NT. (1988). Molecular cloning and sequencing of a pectate lyase gene from Yersinia pseudotuberculosis. J Bacteriol. 1988;170(4):1825-30. DOI:10.1128/jb.170.4.1825-1830.1988 |

5. Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). DOI: 10.1042/BJ20080382